Tue Oct 11 06:56:02 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:56:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5708696 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -18.35200 44.00900 ymin,ymax (A): 21.50400 77.67400 zmin,zma (A): -71.03000 -24.04200 x,y,z range (A): 62.36100 56.17001 46.98800 scale (grids/A): 0.5708696 object centre (A): 12.82850 49.58900 -47.53600 number of atom coordinates read : 2962 total number of charged atoms : 2822 net assigned charge : -1.485992 assigned positive charge : 434.3376 centred at (gu) : 89.28175 90.04499 89.78609 assigned negative charge : -435.8242 centred at (gu) : 89.25706 90.17155 89.78504 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6291 nv = 96 ne = 84 npr = 61477 no. pairs analyzed = 61477 no. exposed pairs = 3637 no. arc points = 25811 no. surface atoms = 1233 nbur = 1729 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 270 mr = 3360 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2567 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8105 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5863575E-10 -2.0282347E-10 midg,1,midg; midg,igrid,midg 1.7299101E-09 -2.2943707E-09 1,midg,midg; igrid,midg,midg -7.3899548E-10 1.3388024E-10 gauss-seidel spectral radius is 0.9841667 estimated iterations to convergence 65 setup time was (sec) 0.6500000 now iterating at: 06:56:03 rms-change max change #iterations 9.1482893E-02 15.42287 at 10iterations 6.8480968E-03 0.9379158 at 20iterations 5.2512059E-04 8.5690498E-02 at 30iterations 3.9319522E-05 6.9885254E-03 at 40iterations 3.1504940E-06 4.8828125E-04 at 50iterations finished qdiffx linear iterations at : 06:56:07 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 3.1504940E-06 4.8828125E-04 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 06:56:07 4.169u 0.278s 0:04.97 89.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:56:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.712609 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -18.35200 44.00900 ymin,ymax (A): 21.50400 77.67400 zmin,zma (A): -71.03000 -24.04200 x,y,z range (A): 62.36100 56.17001 46.98800 scale (grids/A): 1.712609 object centre (A): 12.82850 49.58900 -47.53600 number of atom coordinates read : 2962 total number of charged atoms : 2822 net assigned charge : -1.485992 assigned positive charge : 434.3376 centred at (gu) : 87.84447 90.13435 89.35735 assigned negative charge : -435.8242 centred at (gu) : 87.77070 90.51462 89.35494 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 69068 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25811 grid for indexing accessible points = 1.400000 m= 23282 mr = 47274 m= 3039 mr = 16975 m= 86 mr = 1767 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 338 time to turn everything in is 0.6300000 number of dielectric boundary points 29440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 21870 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5708696 object centre at (A) : 12.82850 49.58900 -47.53600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6434862E-03 1.2176448E-02 midg,1,midg; midg,igrid,midg -5.6028308E-04 3.2725020E-03 1,midg,midg; igrid,midg,midg -1.4657523E-02 -2.5550526E-02 gauss-seidel spectral radius is 0.9983571 estimated iterations to convergence 196 setup time was (sec) 0.9200000 now iterating at: 06:56:09 rms-change max change #iterations 3.649945 161.8567 at 10iterations 1.582668 56.83847 at 20iterations 0.6910297 24.42451 at 30iterations 0.2998939 11.02651 at 40iterations 0.1303163 4.222328 at 50iterations 5.6980394E-02 2.019602 at 60iterations 2.4738917E-02 0.8454647 at 70iterations 1.0772123E-02 0.3843174 at 80iterations 4.6984628E-03 0.1593437 at 90iterations 2.0406193E-03 7.0793003E-02 at 100iterations 8.9072401E-04 2.8650284E-02 at 110iterations 3.8783025E-04 1.5495300E-02 at 120iterations finished qdiffx linear iterations at : 06:56:17 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 3.8783025E-04 1.5495300E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 06:56:18 9.482u 0.316s 0:10.29 95.1% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Tue Oct 11 2011 at 06:56:18 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: HIR 259 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.568913 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -18.35200 44.00900 ymin,ymax (A): 21.50400 77.67400 zmin,zma (A): -71.03000 -24.04200 x,y,z range (A): 62.36100 56.17001 46.98800 scale (grids/A): 2.568913 object centre (A): 12.82850 49.58900 -47.53600 number of atom coordinates read : 2962 total number of charged atoms : 2822 net assigned charge : -1.485992 assigned positive charge : 434.3376 centred at (gu) : 86.76662 90.20132 89.03589 assigned negative charge : -435.8242 centred at (gu) : 86.65594 90.77174 89.03246 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 160262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25811 grid for indexing accessible points = 1.400000 m= 77384 mr = 115253 m= 25481 mr = 62698 m= 4913 mr = 20170 m= 468 mr = 3647 m= 11 mr = 269 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1142 time to turn everything in is 1.550000 number of dielectric boundary points 66482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 22565 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.712609 object centre at (A) : 12.82850 49.58900 -47.53600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1215096 0.1916386 midg,1,midg; midg,igrid,midg -1.5497649E-02 0.1177681 1,midg,midg; igrid,midg,midg -0.2083859 -0.4538891 gauss-seidel spectral radius is 0.9991912 estimated iterations to convergence 278 setup time was (sec) 1.880000 now iterating at: 06:56:20 rms-change max change #iterations 9.102701 293.9698 at 10iterations 5.187806 136.4916 at 20iterations 2.934659 64.04740 at 30iterations 1.655688 40.96376 at 40iterations 0.9309653 18.49120 at 50iterations 0.5243556 10.50621 at 60iterations 0.2946433 6.100296 at 70iterations 0.1650449 3.221601 at 80iterations 9.2546865E-02 1.816986 at 90iterations 5.1874470E-02 0.9634705 at 100iterations 2.9015020E-02 0.5747805 at 110iterations 1.6256332E-02 0.3191404 at 120iterations 9.1221156E-03 0.1815529 at 130iterations 5.0840955E-03 0.1103001 at 140iterations 2.8436217E-03 6.1789036E-02 at 150iterations 1.5947119E-03 3.2331467E-02 at 160iterations 8.9193339E-04 1.6660690E-02 at 170iterations 4.9980043E-04 9.5596313E-03 at 180iterations finished qdiffx linear iterations at : 06:56:34 total time elapsed so far: 15.66000 # loops : 180 mean,max change (kT/e) : 4.9980043E-04 9.5596313E-03 energy calculations done at 15.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.84000 DelPhi exited at 06:56:34 15.846u 0.307s 0:16.48 97.9% 0+0k 0+0io 0pf+0w